So there is no reasonable way a PC navigator can be skilled at navigation? Or more skilled the the team wizard? If my background is that I'm a 30-year old who has been navigating a boat for years (and that was my last PC's background...), it makes sense that a random wizard in the party will be better at it than I am at first level (actually they'd have been tied as I had a +1 Int just for this purpose and that was the highest int in the party)? The game seems to require that PCs be not very good at much of anything other than their class. I was planning on playing someone who was a solid (if not extraordinary) navigator and only recently (like a week ago) become a mildly competent (level 1) fighter. 5e doesn't really support that. I was going to take a level in rogue for expertise (not clear it would apply to navigator's tools, but that's another issue), but we weren't using multi-classing. And I don't know why I _should_ need to take a level in rogue to be a better navigator than a random PC wizard.
And as an engineer, let me tell you that being smart is rarely a substitute for actual training. Anyone who has significant training in navigation is going to be able to actually use the tools of the trade. Someone without said training is going to be a disaster.
5E is like 1E or 2E. If the guy isn't skilled at navigating, he can't do it. You're still thinking like 3E where he gets to roll. If you deem the navigation check too difficult, he doesn't get to roll at all even if he has a 30 intelligence. The new edition specifically discusses skills as in the purview of the DM. He can choose which skill and which ability seems appropriate. For example, for using a rope you could use Dexterity (Water Vehicles) to know how to properly tie a sailor's rope. The idea with skills is that the DM decides according to his experience and/or whim what ability will be used and when it will be used for nearly everything that isn't combat related.
You don't need to take a level of rogue. In 5E if you want to say, "Hey, Mr. DM, I've been navigating since I was a kid, can I have double proficiency in navigation?" The DM either says yes or no. Backgrounds are open-ended and there is plenty of room to do things like that in 5E.
I think people are still stuck thinking like previous editions of 5E. They haven't quite embraced that 5E didn't codify every rule because it knew it couldn't handle corner cases like what you want to do. So it left it up to the DM to allow a player to come up with something that the DM can ok if he deems it is no real disruption to the balance of the game.
So yes, you can make a character that navigates better than the wizard. If the wizard doesn't know how to use navigation tools, he doesn't even get a roll if the DM deems it too difficult. If the DM feels like it, he can give you the equivalent of expertise in a skill as a reward for writing up an background as an extraordinary navigator if no class provides what you're looking for. So 5E does support that as long as you don't get suck in "rules lawyer" mode where you're thinking everything is set in stone. It isn't in 5E. You have a lot of latitude with skills. That was intended the way the skill system was designed.
If you like a hard coded skill system, 5E is not that system. If you like an open-ended skill system that lets you customize skills to fit a player's choices, then 5E works very well. It's when a person reads the skill rules and thinks, "That's it" forgetting all the caveats about DM decides when you can roll, what skills exist, and has very open ended control of the system to work with players that you get full use of the system to do something like make player that is a very good navigator and have it so no one else is even close.